0s autopkgtest [06:55:47]: starting date and time: 2024-05-29 06:55:47+0000 0s autopkgtest [06:55:47]: git checkout: 930f72e5 setup-testbed: don't install 'Recommends' for 'linux-generic' 0s autopkgtest [06:55:47]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work._4t7rr1w/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:dazzdb --apt-upgrade pbdagcon --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=dazzdb/1.0+git20240115.be65e59-1 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos03-arm64-3.secgroup --name adt-oracular-arm64-pbdagcon-20240529-065546-juju-7f2275-prod-proposed-migration-environment-2-129f1a7a-d8a4-44ec-9d68-2f72dcb82803 --image adt/ubuntu-oracular-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 202s autopkgtest [06:59:09]: testbed dpkg architecture: arm64 202s autopkgtest [06:59:09]: testbed apt version: 2.9.3 202s autopkgtest [06:59:09]: @@@@@@@@@@@@@@@@@@@@ test bed setup 203s Get:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease [73.9 kB] 203s Get:2 http://ftpmaster.internal/ubuntu oracular-proposed/main Sources [58.2 kB] 203s Get:3 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse Sources [2568 B] 203s Get:4 http://ftpmaster.internal/ubuntu oracular-proposed/restricted Sources [1964 B] 203s Get:5 http://ftpmaster.internal/ubuntu oracular-proposed/universe Sources [508 kB] 204s Get:6 http://ftpmaster.internal/ubuntu oracular-proposed/main arm64 Packages [142 kB] 204s Get:7 http://ftpmaster.internal/ubuntu oracular-proposed/restricted arm64 Packages [12.3 kB] 204s Get:8 http://ftpmaster.internal/ubuntu oracular-proposed/universe arm64 Packages [569 kB] 204s Get:9 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse arm64 Packages [1972 B] 204s Fetched 1369 kB in 1s (989 kB/s) 206s Reading package lists... 211s Reading package lists... 211s Building dependency tree... 211s Reading state information... 212s Calculating upgrade... 212s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 212s Reading package lists... 212s Building dependency tree... 212s Reading state information... 214s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 216s Hit:1 http://ftpmaster.internal/ubuntu oracular InRelease 216s Hit:2 http://ftpmaster.internal/ubuntu oracular-updates InRelease 216s Hit:3 http://ftpmaster.internal/ubuntu oracular-security InRelease 216s Hit:4 http://ftpmaster.internal/ubuntu oracular-proposed InRelease 221s Reading package lists... 221s Reading package lists... 221s Building dependency tree... 221s Reading state information... 222s Calculating upgrade... 222s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 222s Reading package lists... 222s Building dependency tree... 222s Reading state information... 223s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 227s autopkgtest [06:59:34]: testbed running kernel: Linux 6.8.0-31-generic #31-Ubuntu SMP PREEMPT_DYNAMIC Sat Apr 20 02:32:42 UTC 2024 228s autopkgtest [06:59:35]: @@@@@@@@@@@@@@@@@@@@ apt-source pbdagcon 230s Get:1 http://ftpmaster.internal/ubuntu oracular/universe pbdagcon 0.3+git20180411.c14c422+dfsg-8build3 (dsc) [2475 B] 230s Get:2 http://ftpmaster.internal/ubuntu oracular/universe pbdagcon 0.3+git20180411.c14c422+dfsg-8build3 (tar) [79.8 kB] 230s Get:3 http://ftpmaster.internal/ubuntu oracular/universe pbdagcon 0.3+git20180411.c14c422+dfsg-8build3 (diff) [58.3 kB] 230s gpgv: Signature made Mon Nov 13 17:59:32 2023 UTC 230s gpgv: using RSA key 92978A6E195E4921825F7FF0F34F09744E9F5DD9 230s gpgv: Can't check signature: No public key 230s dpkg-source: warning: cannot verify inline signature for ./pbdagcon_0.3+git20180411.c14c422+dfsg-8build3.dsc: no acceptable signature found 230s autopkgtest [06:59:37]: testing package pbdagcon version 0.3+git20180411.c14c422+dfsg-8build3 230s autopkgtest [06:59:37]: build not needed 231s autopkgtest [06:59:38]: test run-unit-test: preparing testbed 232s Reading package lists... 232s Building dependency tree... 232s Reading state information... 233s Starting pkgProblemResolver with broken count: 0 233s Starting 2 pkgProblemResolver with broken count: 0 233s Done 233s The following additional packages will be installed: 233s blasr daligner dazzdb libaec0 libblasr5.3.5 libhdf5-103-1t64 233s libhdf5-cpp-103-1t64 libhts3t64 libhtscodecs2 libpbbam2.4.0 libpbcopper2.3.0 233s libpbseq libsz2 pbdagcon 233s Suggested packages: 233s dascrubber 233s The following NEW packages will be installed: 233s autopkgtest-satdep blasr daligner dazzdb libaec0 libblasr5.3.5 233s libhdf5-103-1t64 libhdf5-cpp-103-1t64 libhts3t64 libhtscodecs2 libpbbam2.4.0 233s libpbcopper2.3.0 libpbseq libsz2 pbdagcon 234s 0 upgraded, 15 newly installed, 0 to remove and 0 not upgraded. 234s Need to get 4973 kB/4973 kB of archives. 234s After this operation, 17.1 MB of additional disk space will be used. 234s Get:1 /tmp/autopkgtest.YR67jE/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [736 B] 234s Get:2 http://ftpmaster.internal/ubuntu oracular/universe arm64 libaec0 arm64 1.1.3-1 [22.0 kB] 234s Get:3 http://ftpmaster.internal/ubuntu oracular/universe arm64 libsz2 arm64 1.1.3-1 [5254 B] 234s Get:4 http://ftpmaster.internal/ubuntu oracular/universe arm64 libhdf5-103-1t64 arm64 1.10.10+repack-3.1ubuntu4 [1192 kB] 235s Get:5 http://ftpmaster.internal/ubuntu oracular/universe arm64 libhdf5-cpp-103-1t64 arm64 1.10.10+repack-3.1ubuntu4 [121 kB] 235s Get:6 http://ftpmaster.internal/ubuntu oracular/universe arm64 libhtscodecs2 arm64 1.6.0-1build1 [78.0 kB] 235s Get:7 http://ftpmaster.internal/ubuntu oracular/universe arm64 libhts3t64 arm64 1.19+ds-1.1build3 [429 kB] 235s Get:8 http://ftpmaster.internal/ubuntu oracular/universe arm64 libpbcopper2.3.0 arm64 2.3.0+dfsg-2 [516 kB] 235s Get:9 http://ftpmaster.internal/ubuntu oracular/universe arm64 libpbbam2.4.0 arm64 2.4.0+dfsg-1build2 [634 kB] 235s Get:10 http://ftpmaster.internal/ubuntu oracular/universe arm64 libblasr5.3.5 arm64 5.3.5+dfsg-6build5 [1207 kB] 235s Get:11 http://ftpmaster.internal/ubuntu oracular/universe arm64 libpbseq arm64 5.3.5+dfsg-6build5 [3064 B] 235s Get:12 http://ftpmaster.internal/ubuntu oracular/universe arm64 blasr arm64 5.3.5+dfsg-6build5 [213 kB] 235s Get:13 http://ftpmaster.internal/ubuntu oracular/universe arm64 daligner arm64 1.0+git20240119.335105d-2 [155 kB] 236s Get:14 http://ftpmaster.internal/ubuntu oracular-proposed/universe arm64 dazzdb arm64 1.0+git20240115.be65e59-1 [146 kB] 236s Get:15 http://ftpmaster.internal/ubuntu oracular/universe arm64 pbdagcon arm64 0.3+git20180411.c14c422+dfsg-8build3 [252 kB] 236s Fetched 4973 kB in 2s (2381 kB/s) 237s Selecting previously unselected package libaec0:arm64. 238s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78195 files and directories currently installed.) 238s Preparing to unpack .../00-libaec0_1.1.3-1_arm64.deb ... 238s Unpacking libaec0:arm64 (1.1.3-1) ... 239s Selecting previously unselected package libsz2:arm64. 239s Preparing to unpack .../01-libsz2_1.1.3-1_arm64.deb ... 239s Unpacking libsz2:arm64 (1.1.3-1) ... 239s Selecting previously unselected package libhdf5-103-1t64:arm64. 239s Preparing to unpack .../02-libhdf5-103-1t64_1.10.10+repack-3.1ubuntu4_arm64.deb ... 239s Unpacking libhdf5-103-1t64:arm64 (1.10.10+repack-3.1ubuntu4) ... 240s Selecting previously unselected package libhdf5-cpp-103-1t64:arm64. 240s Preparing to unpack .../03-libhdf5-cpp-103-1t64_1.10.10+repack-3.1ubuntu4_arm64.deb ... 240s Unpacking libhdf5-cpp-103-1t64:arm64 (1.10.10+repack-3.1ubuntu4) ... 240s Selecting previously unselected package libhtscodecs2:arm64. 240s Preparing to unpack .../04-libhtscodecs2_1.6.0-1build1_arm64.deb ... 240s Unpacking libhtscodecs2:arm64 (1.6.0-1build1) ... 240s Selecting previously unselected package libhts3t64:arm64. 240s Preparing to unpack .../05-libhts3t64_1.19+ds-1.1build3_arm64.deb ... 240s Unpacking libhts3t64:arm64 (1.19+ds-1.1build3) ... 240s Selecting previously unselected package libpbcopper2.3.0:arm64. 240s Preparing to unpack .../06-libpbcopper2.3.0_2.3.0+dfsg-2_arm64.deb ... 240s Unpacking libpbcopper2.3.0:arm64 (2.3.0+dfsg-2) ... 240s Selecting previously unselected package libpbbam2.4.0:arm64. 240s Preparing to unpack .../07-libpbbam2.4.0_2.4.0+dfsg-1build2_arm64.deb ... 240s Unpacking libpbbam2.4.0:arm64 (2.4.0+dfsg-1build2) ... 240s Selecting previously unselected package libblasr5.3.5:arm64. 240s Preparing to unpack .../08-libblasr5.3.5_5.3.5+dfsg-6build5_arm64.deb ... 240s Unpacking libblasr5.3.5:arm64 (5.3.5+dfsg-6build5) ... 240s Selecting previously unselected package libpbseq:arm64. 240s Preparing to unpack .../09-libpbseq_5.3.5+dfsg-6build5_arm64.deb ... 240s Unpacking libpbseq:arm64 (5.3.5+dfsg-6build5) ... 240s Selecting previously unselected package blasr. 240s Preparing to unpack .../10-blasr_5.3.5+dfsg-6build5_arm64.deb ... 240s Unpacking blasr (5.3.5+dfsg-6build5) ... 240s Selecting previously unselected package daligner. 240s Preparing to unpack .../11-daligner_1.0+git20240119.335105d-2_arm64.deb ... 240s Unpacking daligner (1.0+git20240119.335105d-2) ... 240s Selecting previously unselected package dazzdb. 240s Preparing to unpack .../12-dazzdb_1.0+git20240115.be65e59-1_arm64.deb ... 240s Unpacking dazzdb (1.0+git20240115.be65e59-1) ... 240s Selecting previously unselected package pbdagcon. 240s Preparing to unpack .../13-pbdagcon_0.3+git20180411.c14c422+dfsg-8build3_arm64.deb ... 240s Unpacking pbdagcon (0.3+git20180411.c14c422+dfsg-8build3) ... 240s Selecting previously unselected package autopkgtest-satdep. 240s Preparing to unpack .../14-1-autopkgtest-satdep.deb ... 240s Unpacking autopkgtest-satdep (0) ... 240s Setting up libhtscodecs2:arm64 (1.6.0-1build1) ... 240s Setting up libaec0:arm64 (1.1.3-1) ... 240s Setting up dazzdb (1.0+git20240115.be65e59-1) ... 240s Setting up daligner (1.0+git20240119.335105d-2) ... 240s Setting up libhts3t64:arm64 (1.19+ds-1.1build3) ... 240s Setting up libsz2:arm64 (1.1.3-1) ... 240s Setting up libpbcopper2.3.0:arm64 (2.3.0+dfsg-2) ... 240s Setting up libpbbam2.4.0:arm64 (2.4.0+dfsg-1build2) ... 240s Setting up libhdf5-103-1t64:arm64 (1.10.10+repack-3.1ubuntu4) ... 240s Setting up libhdf5-cpp-103-1t64:arm64 (1.10.10+repack-3.1ubuntu4) ... 240s Setting up libblasr5.3.5:arm64 (5.3.5+dfsg-6build5) ... 240s Setting up libpbseq:arm64 (5.3.5+dfsg-6build5) ... 240s Setting up blasr (5.3.5+dfsg-6build5) ... 240s Setting up pbdagcon (0.3+git20180411.c14c422+dfsg-8build3) ... 240s Setting up autopkgtest-satdep (0) ... 240s Processing triggers for man-db (2.12.1-1) ... 241s Processing triggers for libc-bin (2.39-0ubuntu8.1) ... 246s (Reading database ... 78370 files and directories currently installed.) 246s Removing autopkgtest-satdep (0) ... 247s autopkgtest [06:59:54]: test run-unit-test: [----------------------- 247s Test 1 248s [INFO] 2024-05-29T06:59:55 [blasr] started. 248s [INFO] 2024-05-29T06:59:55 [blasr] ended. 248s 2024-05-29 06:59:55,507 INFO [default] Multi-threaded. Input: mapped.m5, Threads: 4 248s 2024-05-29 06:59:55,509 DEBUG [Reader] [ubuntu@unknown-host] [FUNCTION] [FILE:0] Consensus candidate: random 248s 2024-05-29 06:59:55,510 INFO [Consensus] Consensus calling: random Alignments: 21 248s consensus.fasta: OK 248s mapped.m5: OK 248s queries.fasta: OK 248s target.dam: FAILED 248s target.fasta: OK 248s md5sum: WARNING: 1 computed checksum did NOT match 248s autopkgtest [06:59:55]: test run-unit-test: -----------------------] 249s autopkgtest [06:59:56]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 249s run-unit-test FAIL non-zero exit status 1 250s autopkgtest [06:59:57]: @@@@@@@@@@@@@@@@@@@@ summary 250s run-unit-test FAIL non-zero exit status 1 299s flock: timeout while waiting to get lock 299s Creating nova instance adt-oracular-arm64-pbdagcon-20240529-065546-juju-7f2275-prod-proposed-migration-environment-2-129f1a7a-d8a4-44ec-9d68-2f72dcb82803 from image adt/ubuntu-oracular-arm64-server-20240529.img (UUID 85bf347b-2b61-4c86-89a2-abeb29ee5d55)...